Start: 2022-09-30 15:18:15 GMT [testing] Package: liballelecount-perl Source: allelecount Version: 4.3.0-1.1 Installed-Size: 81 Maintainer: Debian Med Packaging Team Architecture: all Depends: perl:any, libconst-fast-perl, libdevel-cover-perl, libfile-slurp-perl, libfile-which-perl, libipc-system-simple-perl, libpod-coverage-perl, libtest-fatal-perl, libtry-tiny-perl, libjson-perl Description: Perl interface to NGS copy number algorithms Homepage: https://github.com/cancerit/alleleCount Description-md5: 3643df2ba0a59c066ab75e82c8e21f1a Section: perl Priority: optional Filename: pool/main/a/allelecount/liballelecount-perl_4.3.0-1.1_all.deb Size: 25032 MD5sum: 1cf5b91cd1a75a6690663f123ce5b336 SHA256: e5ebf8ac140dfac9d086a84c2bdd48adf6702203d171cd600982da749b2ccf27 [sid] Package: liballelecount-perl Source: allelecount Version: 4.3.0-2 Installed-Size: 81 Maintainer: Debian Med Packaging Team Architecture: all Depends: perl:any, libconst-fast-perl, libdevel-cover-perl, libfile-slurp-perl, libfile-which-perl, libipc-system-simple-perl, libpod-coverage-perl, libtest-fatal-perl, libtry-tiny-perl, libjson-perl Description: Perl interface to NGS copy number algorithms Homepage: https://github.com/cancerit/alleleCount Description-md5: 3643df2ba0a59c066ab75e82c8e21f1a Section: perl Priority: optional Filename: pool/main/a/allelecount/liballelecount-perl_4.3.0-2_all.deb Size: 25020 MD5sum: 7fca00320975ab41b29a9960f565a413 SHA256: 29f56c7ab093bc94845e899c3a9c9b05dee2ba5fd153801e3dea4f8818a2b0c5 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt liballelecount-perl=4.3.0-2 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.1.5 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt liballelecount-perl=4.3.0-2 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-18-amd64 #1 SMP Debian 5.10.140-1 (2022-09-02) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpic6osoyu 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpic6osoyu 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz'] 0m2.1s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz'] 0m2.1s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpic6osoyu/proc'] 0m2.1s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpic6osoyu/proc'] 0m2.1s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpic6osoyu/dev/pts'] 0m2.1s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpic6osoyu/dev/pts'] 0m2.1s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpic6osoyu/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpic6osoyu/dev/ptmx'] 0m2.1s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpic6osoyu/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpic6osoyu/dev/ptmx'] 0m2.1s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpic6osoyu/dev/console'] 0m2.1s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpic6osoyu/dev/console'] 0m2.1s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpic6osoyu/dev/shm'] 0m2.1s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpic6osoyu/dev/shm'] 0m2.1s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m2.1s DEBUG: Created policy-rc.d and chmodded it. 0m2.1s DEBUG: Created resolv.conf. 0m2.1s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpic6osoyu/tmp/scripts/ 0m2.1s INFO: Running scripts post_chroot_unpack 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'apt-get', 'update'] 0m4.1s DUMP: Get:1 http://deb.debian.org/debian bookworm InRelease [161 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 Packages [8461 kB] Get:3 http://deb.debian.org/debian bookworm/main Translation-en [5762 kB] Fetched 14.4 MB in 1s (10.0 MB/s) Reading package lists... 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'apt-get', 'update'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'apt-get', '-yf', 'dist-upgrade'] 0m5.7s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: libc-bin libc6 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 3763 kB of archives. After this operation, 636 kB disk space will be freed. Get:1 http://deb.debian.org/debian bookworm/main amd64 libc6 amd64 2.35-1 [2941 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libc-bin amd64 2.35-1 [822 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 3763 kB in 0s (54.2 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8606 files and directories currently installed.) Preparing to unpack .../libc6_2.35-1_amd64.deb ... Unpacking libc6:amd64 (2.35-1) over (2.34-8) ... Setting up libc6:amd64 (2.35-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8605 files and directories currently installed.) Preparing to unpack .../libc-bin_2.35-1_amd64.deb ... Unpacking libc-bin (2.35-1) over (2.34-8) ... Setting up libc-bin (2.35-1) ... 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'apt-get', '-yf', 'dist-upgrade'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m6.0s DUMP: 32402edaa6effca61dc47c858ee573ed - 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m6.0s INFO: Running scripts post_setup 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/post_setup_dummy_users'] 0m6.4s DUMP: useradd warning: dummy100's uid 100 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1000's uid 1000 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1001's uid 1001 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1002's uid 1002 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1003's uid 1003 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1004's uid 1004 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1005's uid 1005 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1006's uid 1006 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1007's uid 1007 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1008's uid 1008 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1009's uid 1009 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. useradd warning: dummy1010's uid 1010 outside of the SYS_UID_MIN 101 and SYS_UID_MAX 999 range. 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/post_setup_dummy_users'] 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/post_setup_forbid_home'] 0m6.4s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/post_setup_forbid_home'] 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/post_setup_force-unsafe-io'] 0m6.5s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/post_setup_force-unsafe-io'] 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/post_setup_minimize'] 0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/post_setup_minimize'] 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/post_setup_squeeze-backports'] 0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/post_setup_squeeze-backports'] 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/post_setup_zz_backports'] 0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/post_setup_zz_backports'] 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m6.5s DUMP: install ok installed adduser adduser 3.129 install ok installed apt apt 2.5.2 install ok installed base-files base-files 12.2 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2~rc2-2 install ok installed bsdutils bsdutils 1:2.38.1-1 install ok installed coreutils coreutils 8.32-4.1+b1 install ok installed dash dash 0.5.11+git20210903+057cd650a4ed-9 install ok installed debconf debconf 1.5.79 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1 install ok installed debianutils debianutils 5.7-0.3 install ok installed diffutils diffutils 1:3.8-1 install ok installed dpkg dpkg 1.21.9 install ok installed e2fsprogs e2fsprogs 1.46.6~rc1-1 install ok installed findutils findutils 4.9.0-3 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-3 install ok installed gpgv gpgv 2.2.39-1 install ok installed grep grep 3.7-1 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-1 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.5.2 install ok installed libattr1:amd64 libattr1 1:2.5.1-1 install ok installed libaudit-common libaudit-common 1:3.0.7-1.1 install ok installed libaudit1:amd64 libaudit1 1:3.0.7-1.1 install ok installed libblkid1:amd64 libblkid1 2.38.1-1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.35-1 install ok installed libc6:amd64 libc6 2.35-1 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b1 install ok installed libcap2:amd64 libcap2 1:2.44-1 install ok installed libcom-err2:amd64 libcom-err2 1.46.6~rc1-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.28-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.10 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.264 install ok installed libext2fs2:amd64 libext2fs2 1.46.6~rc1-1 install ok installed libffi8:amd64 libffi8 3.4.2-4 install ok installed libfile-find-rule-perl libfile-find-rule-perl 0.34-2 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-3 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-2 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.23-2 install ok installed libgdbm6:amd64 libgdbm6 1.23-2 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1 install ok installed libgnutls30:amd64 libgnutls30 3.7.7-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.45-2 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.2.5-2.1 install ok installed libmount1:amd64 libmount1 2.38.1-1 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-2 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-2 install ok installed libpam-runtime libpam-runtime 1.5.2-2 install ok installed libpam0g:amd64 libpam0g 1.5.2-2 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.40-1 install ok installed libpcre3:amd64 libpcre3 2:8.39-14 install ok installed libperl5.34:amd64 libperl5.34 5.34.0-5 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b1 install ok installed libselinux1:amd64 libselinux1 3.4-1+b2 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b2 install ok installed libsepol2:amd64 libsepol2 3.4-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-1 install ok installed libss2:amd64 libss2 1.46.6~rc1-1 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-3 install ok installed libsystemd0:amd64 libsystemd0 251.4-3 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtext-glob-perl libtext-glob-perl 0.11-2 install ok installed libtinfo6:amd64 libtinfo6 6.3+20220423-2 install ok installed libudev1:amd64 libudev1 251.4-3 install ok installed libunistring2:amd64 libunistring2 1.0-1 install ok installed libuuid1:amd64 libuuid1 2.38.1-1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.2+dfsg-1 install ok installed login login 1:4.11.1+dfsg1-2 install ok installed logsave logsave 1.46.6~rc1-1 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-1 install ok installed ncurses-base ncurses-base 6.3+20220423-2 install ok installed ncurses-bin ncurses-bin 6.3+20220423-2 install ok installed passwd passwd 1:4.11.1+dfsg1-2 install ok installed perl perl 5.34.0-5 install ok installed perl-base perl-base 5.34.0-5 install ok installed perl-modules-5.34 perl-modules-5.34 5.34.0-5 install ok installed sed sed 4.8-1 install ok installed sysvinit-utils sysvinit-utils 3.05-6 install ok installed tar tar 1.34+dfsg-1 install ok installed tzdata tzdata 2022c-1 install ok installed usr-is-merged usr-is-merged 31 install ok installed usrmerge usrmerge 31 install ok installed util-linux util-linux 2.38.1-1 install ok installed util-linux-extra util-linux-extra 2.38.1-1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-4.1 0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m6.5s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m6.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpic6osoyu'] 0m6.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpic6osoyu'] 0m6.9s INFO: Running scripts is_testable 0m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/is_testable_uninstallable'] 0m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/is_testable_uninstallable'] 0m6.9s INFO: Running scripts pre_test 0m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_test_exceptions'] 0m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_test_exceptions'] 0m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_test_root_password'] 0m6.9s DUMP: New password: Retype new password: passwd: password updated successfully 0m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_test_root_password'] 0m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'apt-cache', 'show', '--no-all-versions', 'liballelecount-perl'] 0m7.1s DUMP: Package: liballelecount-perl Source: allelecount Version: 4.3.0-1.1 Installed-Size: 81 Maintainer: Debian Med Packaging Team Architecture: all Depends: perl:any, libconst-fast-perl, libdevel-cover-perl, libfile-slurp-perl, libfile-which-perl, libipc-system-simple-perl, libpod-coverage-perl, libtest-fatal-perl, libtry-tiny-perl, libjson-perl Description-en: Perl interface to NGS copy number algorithms Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each allele [ACGT] at that location (given any filter settings). . The alleleCount package primarily exists to prevent code duplication between some other projects, specifically AscatNGS and Battenberg. . This package provided the Perl interface to alleleCounter providing Sanger::CGP::AlleleCount::Genotype. Description-md5: 3643df2ba0a59c066ab75e82c8e21f1a Homepage: https://github.com/cancerit/alleleCount Section: perl Priority: optional Filename: pool/main/a/allelecount/liballelecount-perl_4.3.0-1.1_all.deb Size: 25032 MD5sum: 1cf5b91cd1a75a6690663f123ce5b336 SHA256: e5ebf8ac140dfac9d086a84c2bdd48adf6702203d171cd600982da749b2ccf27 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'apt-cache', 'show', '--no-all-versions', 'liballelecount-perl'] 0m7.1s INFO: apt-cache knows about the following packages: liballelecount-perl 0m7.1s INFO: Running scripts pre_install 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_install_database-server'] 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_install_database-server'] 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_install_exceptions'] 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_install_exceptions'] 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_install_extras'] 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_install_extras'] 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_install_foreign_architecture'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_install_foreign_architecture'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'apt-cache', 'policy'] 0m7.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release o=Debian,a=testing,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'apt-cache', 'policy'] 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'apt-cache', 'policy', 'liballelecount-perl'] 0m7.3s DUMP: liballelecount-perl: Installed: (none) Candidate: 4.3.0-1.1 Version table: 4.3.0-1.1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'apt-cache', 'policy', 'liballelecount-perl'] 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'apt-get', '-y', 'install', 'liballelecount-perl'] 0m8.5s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libb-debug-perl libconst-fast-perl libdata-optlist-perl libdevel-cover-perl libdevel-symdump-perl libfile-slurp-perl libfile-which-perl libhtml-parser-perl libhtml-tagset-perl libipc-system-simple-perl libjson-perl libparams-util-perl libpod-coverage-perl libpod-parser-perl libregexp-ipv6-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-install-perl libtest-fatal-perl libtry-tiny-perl liburi-perl Suggested packages: libbrowser-open-perl libcapture-tiny-perl libclass-xsaccessor-perl libjson-maybexs-perl libmoo-perl libnamespace-clean-perl libppi-html-perl | perltidy libsereal-decoder-perl libsereal-encoder-perl libterm-size-perl libtest-differences-perl libdata-dump-perl libsub-name-perl libbusiness-isbn-perl libwww-perl Recommended packages: gcc libtemplate-perl libhttp-message-perl libjson-xs-perl The following NEW packages will be installed: liballelecount-perl libb-debug-perl libconst-fast-perl libdata-optlist-perl libdevel-cover-perl libdevel-symdump-perl libfile-slurp-perl libfile-which-perl libhtml-parser-perl libhtml-tagset-perl libipc-system-simple-perl libjson-perl libparams-util-perl libpod-coverage-perl libpod-parser-perl libregexp-ipv6-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-install-perl libtest-fatal-perl libtry-tiny-perl liburi-perl 0 upgraded, 22 newly installed, 0 to remove and 0 not upgraded. Need to get 906 kB of archives. After this operation, 2509 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 libparams-util-perl amd64 1.102-1+b2 [25.7 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libsub-install-perl all 0.928-2 [11.0 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libdata-optlist-perl all 0.112-1 [11.8 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 libsub-exporter-perl all 0.988-1 [51.9 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 libsub-exporter-progressive-perl all 0.001013-2 [8044 B] Get:6 http://deb.debian.org/debian bookworm/main amd64 libconst-fast-perl all 0.014-2 [8792 B] Get:7 http://deb.debian.org/debian bookworm/main amd64 libb-debug-perl all 1.26-2 [11.4 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 libhtml-tagset-perl all 3.20-5 [13.1 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 libregexp-ipv6-perl all 0.03-3 [5212 B] Get:10 http://deb.debian.org/debian bookworm/main amd64 liburi-perl all 5.12-1 [93.7 kB] Get:11 http://deb.debian.org/debian bookworm/main amd64 libhtml-parser-perl amd64 3.78-1 [105 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 libdevel-cover-perl amd64 1.38-1 [197 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 libfile-slurp-perl all 9999.32-1 [28.1 kB] Get:14 http://deb.debian.org/debian bookworm/main amd64 libfile-which-perl all 1.27-1 [17.3 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 libipc-system-simple-perl all 1.30-1 [28.2 kB] Get:16 http://deb.debian.org/debian bookworm/main amd64 libdevel-symdump-perl all 2.18-4 [17.5 kB] Get:17 http://deb.debian.org/debian bookworm/main amd64 libpod-parser-perl all 1.65-1 [96.3 kB] Get:18 http://deb.debian.org/debian bookworm/main amd64 libpod-coverage-perl all 0.23-2 [22.1 kB] Get:19 http://deb.debian.org/debian bookworm/main amd64 libtry-tiny-perl all 0.31-1 [24.2 kB] Get:20 http://deb.debian.org/debian bookworm/main amd64 libtest-fatal-perl all 0.016-1 [13.3 kB] Get:21 http://deb.debian.org/debian bookworm/main amd64 libjson-perl all 4.09000-1 [90.5 kB] Get:22 http://deb.debian.org/debian bookworm/main amd64 liballelecount-perl all 4.3.0-1.1 [25.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 906 kB in 0s (6547 kB/s) Selecting previously unselected package libparams-util-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8606 files and directories currently installed.) Preparing to unpack .../00-libparams-util-perl_1.102-1+b2_amd64.deb ... Unpacking libparams-util-perl (1.102-1+b2) ... Selecting previously unselected package libsub-install-perl. Preparing to unpack .../01-libsub-install-perl_0.928-2_all.deb ... Unpacking libsub-install-perl (0.928-2) ... Selecting previously unselected package libdata-optlist-perl. Preparing to unpack .../02-libdata-optlist-perl_0.112-1_all.deb ... Unpacking libdata-optlist-perl (0.112-1) ... Selecting previously unselected package libsub-exporter-perl. Preparing to unpack .../03-libsub-exporter-perl_0.988-1_all.deb ... Unpacking libsub-exporter-perl (0.988-1) ... Selecting previously unselected package libsub-exporter-progressive-perl. Preparing to unpack .../04-libsub-exporter-progressive-perl_0.001013-2_all.deb ... Unpacking libsub-exporter-progressive-perl (0.001013-2) ... Selecting previously unselected package libconst-fast-perl. Preparing to unpack .../05-libconst-fast-perl_0.014-2_all.deb ... Unpacking libconst-fast-perl (0.014-2) ... Selecting previously unselected package libb-debug-perl. Preparing to unpack .../06-libb-debug-perl_1.26-2_all.deb ... Unpacking libb-debug-perl (1.26-2) ... Selecting previously unselected package libhtml-tagset-perl. Preparing to unpack .../07-libhtml-tagset-perl_3.20-5_all.deb ... Unpacking libhtml-tagset-perl (3.20-5) ... Selecting previously unselected package libregexp-ipv6-perl. Preparing to unpack .../08-libregexp-ipv6-perl_0.03-3_all.deb ... Unpacking libregexp-ipv6-perl (0.03-3) ... Selecting previously unselected package liburi-perl. Preparing to unpack .../09-liburi-perl_5.12-1_all.deb ... Unpacking liburi-perl (5.12-1) ... Selecting previously unselected package libhtml-parser-perl:amd64. Preparing to unpack .../10-libhtml-parser-perl_3.78-1_amd64.deb ... Unpacking libhtml-parser-perl:amd64 (3.78-1) ... Selecting previously unselected package libdevel-cover-perl. Preparing to unpack .../11-libdevel-cover-perl_1.38-1_amd64.deb ... Unpacking libdevel-cover-perl (1.38-1) ... Selecting previously unselected package libfile-slurp-perl. Preparing to unpack .../12-libfile-slurp-perl_9999.32-1_all.deb ... Unpacking libfile-slurp-perl (9999.32-1) ... Selecting previously unselected package libfile-which-perl. Preparing to unpack .../13-libfile-which-perl_1.27-1_all.deb ... Unpacking libfile-which-perl (1.27-1) ... Selecting previously unselected package libipc-system-simple-perl. Preparing to unpack .../14-libipc-system-simple-perl_1.30-1_all.deb ... Unpacking libipc-system-simple-perl (1.30-1) ... Selecting previously unselected package libdevel-symdump-perl. Preparing to unpack .../15-libdevel-symdump-perl_2.18-4_all.deb ... Unpacking libdevel-symdump-perl (2.18-4) ... Selecting previously unselected package libpod-parser-perl. Preparing to unpack .../16-libpod-parser-perl_1.65-1_all.deb ... Adding 'diversion of /usr/bin/podselect to /usr/bin/podselect.bundled by libpod-parser-perl' Adding 'diversion of /usr/share/man/man1/podselect.1.gz to /usr/share/man/man1/podselect.bundled.1.gz by libpod-parser-perl' Unpacking libpod-parser-perl (1.65-1) ... Selecting previously unselected package libpod-coverage-perl. Preparing to unpack .../17-libpod-coverage-perl_0.23-2_all.deb ... Unpacking libpod-coverage-perl (0.23-2) ... Selecting previously unselected package libtry-tiny-perl. Preparing to unpack .../18-libtry-tiny-perl_0.31-1_all.deb ... Unpacking libtry-tiny-perl (0.31-1) ... Selecting previously unselected package libtest-fatal-perl. Preparing to unpack .../19-libtest-fatal-perl_0.016-1_all.deb ... Unpacking libtest-fatal-perl (0.016-1) ... Selecting previously unselected package libjson-perl. Preparing to unpack .../20-libjson-perl_4.09000-1_all.deb ... Unpacking libjson-perl (4.09000-1) ... Selecting previously unselected package liballelecount-perl. Preparing to unpack .../21-liballelecount-perl_4.3.0-1.1_all.deb ... Unpacking liballelecount-perl (4.3.0-1.1) ... Setting up libfile-which-perl (1.27-1) ... Setting up libfile-slurp-perl (9999.32-1) ... Setting up libhtml-tagset-perl (3.20-5) ... Setting up libtry-tiny-perl (0.31-1) ... Setting up libtest-fatal-perl (0.016-1) ... Setting up libb-debug-perl (1.26-2) ... Setting up libsub-install-perl (0.928-2) ... Setting up libipc-system-simple-perl (1.30-1) ... Setting up libpod-parser-perl (1.65-1) ... Setting up libparams-util-perl (1.102-1+b2) ... Setting up libsub-exporter-progressive-perl (0.001013-2) ... Setting up libregexp-ipv6-perl (0.03-3) ... Setting up libjson-perl (4.09000-1) ... Setting up libdevel-symdump-perl (2.18-4) ... Setting up liburi-perl (5.12-1) ... Setting up libpod-coverage-perl (0.23-2) ... Setting up libdata-optlist-perl (0.112-1) ... Setting up libhtml-parser-perl:amd64 (3.78-1) ... Setting up libsub-exporter-perl (0.988-1) ... Setting up libdevel-cover-perl (1.38-1) ... Setting up libconst-fast-perl (0.014-2) ... Setting up liballelecount-perl (4.3.0-1.1) ... 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'apt-get', '-y', 'install', 'liballelecount-perl'] 0m8.5s INFO: Running scripts post_install 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/post_install_exceptions'] 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/post_install_exceptions'] 0m8.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpic6osoyu'] 0m9.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpic6osoyu'] 0m9.1s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpic6osoyu to sid 0m9.1s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m9.1s INFO: Running scripts pre_distupgrade 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_distupgrade_exceptions'] 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_distupgrade_exceptions'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'apt-get', 'update'] 0m12.1s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [158 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9349 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [6910 kB] Fetched 16.4 MB in 2s (7025 kB/s) Reading package lists... 0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'apt-get', 'update'] 0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'apt-get', '-yf', 'dist-upgrade'] 0m14.5s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt bash coreutils grep liballelecount-perl libapt-pkg6.0 libffi8 tzdata usr-is-merged usrmerge 10 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 7762 kB of archives. After this operation, 764 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 bash amd64 5.2-1 [1524 kB] Get:2 http://deb.debian.org/debian sid/main amd64 coreutils amd64 9.1-1 [2897 kB] Get:3 http://deb.debian.org/debian sid/main amd64 grep amd64 3.8-2 [432 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0 amd64 2.5.3 [1044 kB] Get:5 http://deb.debian.org/debian sid/main amd64 apt amd64 2.5.3 [1505 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libffi8 amd64 3.4.3-2 [26.1 kB] Get:7 http://deb.debian.org/debian sid/main amd64 usr-is-merged all 32 [5524 B] Get:8 http://deb.debian.org/debian sid/main amd64 usrmerge all 32 [13.2 kB] Get:9 http://deb.debian.org/debian sid/main amd64 tzdata all 2022d-1 [290 kB] Get:10 http://deb.debian.org/debian sid/main amd64 liballelecount-perl all 4.3.0-2 [25.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 7762 kB in 0s (65.3 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9035 files and directories currently installed.) Preparing to unpack .../archives/bash_5.2-1_amd64.deb ... Unpacking bash (5.2-1) over (5.2~rc2-2) ... Setting up bash (5.2-1) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9036 files and directories currently installed.) Preparing to unpack .../archives/usrmerge_32_all.deb ... Unpacking usrmerge (32) over (31) ... Setting up usrmerge (32) ... W: /etc/unsupported-skip-usrmerge-conversion exists. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9036 files and directories currently installed.) Preparing to unpack .../tzdata_2022d-1_all.deb ... Unpacking tzdata (2022d-1) over (2022c-1) ... Preparing to unpack .../liballelecount-perl_4.3.0-2_all.deb ... Unpacking liballelecount-perl (4.3.0-2) over (4.3.0-1.1) ... Setting up liballelecount-perl (4.3.0-2) ... Setting up tzdata (2022d-1) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Sep 30 15:18:30 UTC 2022. Universal Time is now: Fri Sep 30 15:18:30 UTC 2022. Run 'dpkg-reconfigure tzdata' if you wish to change it. Processing triggers for libc-bin (2.35-1) ... Processing triggers for debianutils (5.7-0.3) ... 0m14.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'apt-get', '-yf', 'dist-upgrade'] 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m15.3s DUMP: c513fce8a0691ff5e0b57b15039588d1 - 0m15.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m15.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'apt-cache', 'show', '--no-all-versions', 'liballelecount-perl'] 0m15.5s DUMP: Package: liballelecount-perl Source: allelecount Version: 4.3.0-2 Installed-Size: 81 Maintainer: Debian Med Packaging Team Architecture: all Depends: perl:any, libconst-fast-perl, libdevel-cover-perl, libfile-slurp-perl, libfile-which-perl, libipc-system-simple-perl, libpod-coverage-perl, libtest-fatal-perl, libtry-tiny-perl, libjson-perl Description-en: Perl interface to NGS copy number algorithms Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each allele [ACGT] at that location (given any filter settings). . The alleleCount package primarily exists to prevent code duplication between some other projects, specifically AscatNGS and Battenberg. . This package provided the Perl interface to alleleCounter providing Sanger::CGP::AlleleCount::Genotype. Description-md5: 3643df2ba0a59c066ab75e82c8e21f1a Homepage: https://github.com/cancerit/alleleCount Section: perl Priority: optional Filename: pool/main/a/allelecount/liballelecount-perl_4.3.0-2_all.deb Size: 25020 MD5sum: 7fca00320975ab41b29a9960f565a413 SHA256: 29f56c7ab093bc94845e899c3a9c9b05dee2ba5fd153801e3dea4f8818a2b0c5 0m15.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'apt-cache', 'show', '--no-all-versions', 'liballelecount-perl'] 0m15.5s INFO: apt-cache knows about the following packages: liballelecount-perl 0m15.5s INFO: Running scripts pre_install 0m15.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_install_database-server'] 0m15.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_install_database-server'] 0m15.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_install_exceptions'] 0m15.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_install_exceptions'] 0m15.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_install_extras'] 0m15.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_install_extras'] 0m15.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_install_foreign_architecture'] 0m15.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_install_foreign_architecture'] 0m15.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m15.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m15.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'apt-cache', 'policy'] 0m15.6s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m15.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'apt-cache', 'policy'] 0m15.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'apt-cache', 'policy', 'liballelecount-perl'] 0m15.7s DUMP: liballelecount-perl: Installed: 4.3.0-2 Candidate: 4.3.0-2 Version table: *** 4.3.0-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m15.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'apt-cache', 'policy', 'liballelecount-perl'] 0m15.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'apt-get', '-y', 'install', 'liballelecount-perl'] 0m16.1s DUMP: Reading package lists... Building dependency tree... Reading state information... liballelecount-perl is already the newest version (4.3.0-2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m16.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'apt-get', '-y', 'install', 'liballelecount-perl'] 0m16.1s INFO: Running scripts post_install 0m16.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/post_install_exceptions'] 0m16.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/post_install_exceptions'] 0m16.2s INFO: Running scripts post_distupgrade 0m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m16.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/post_distupgrade_exceptions'] 0m16.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/post_distupgrade_exceptions'] 0m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m16.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m16.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/post_distupgrade_zz_backports'] 0m16.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/post_distupgrade_zz_backports'] 0m16.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpic6osoyu'] 0m16.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpic6osoyu'] 0m16.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpic6osoyu'] 0m17.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpic6osoyu'] 0m17.2s INFO: Running scripts pre_install 0m17.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_install_database-server'] 0m17.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_install_database-server'] 0m17.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_install_exceptions'] 0m17.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_install_exceptions'] 0m17.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_install_extras'] 0m17.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_install_extras'] 0m17.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_install_foreign_architecture'] 0m17.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_install_foreign_architecture'] 0m17.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m17.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m17.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'apt-cache', 'policy'] 0m17.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m17.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'apt-cache', 'policy'] 0m17.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'apt-cache', 'policy', 'liballelecount-perl'] 0m17.3s DUMP: liballelecount-perl: Installed: 4.3.0-2 Candidate: 4.3.0-2 Version table: *** 4.3.0-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m17.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'apt-cache', 'policy', 'liballelecount-perl'] 0m17.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'apt-get', '-y', 'install', 'liballelecount-perl=4.3.0-2'] 0m17.8s DUMP: Reading package lists... Building dependency tree... Reading state information... liballelecount-perl is already the newest version (4.3.0-2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m17.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'apt-get', '-y', 'install', 'liballelecount-perl=4.3.0-2'] 0m17.8s INFO: Running scripts post_install 0m17.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/post_install_exceptions'] 0m17.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/post_install_exceptions'] 0m17.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpic6osoyu'] 0m18.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpic6osoyu'] 0m18.6s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', '-ac', '--ignore-obsolete'] 0m19.3s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', '-ac', '--ignore-obsolete'] 0m19.3s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m19.3s DUMP: 0.15.6 0m19.3s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m19.3s INFO: Running adequate version 0.15.6 now. 0m19.3s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'liballelecount-perl'] 0m19.4s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'liballelecount-perl'] 0m19.4s INFO: Running scripts pre_remove 0m19.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m19.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m19.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m19.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m19.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m20.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m20.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m20.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m20.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m20.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m20.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_remove_exceptions'] 0m20.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/pre_remove_exceptions'] 0m20.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m20.3s DUMP: install ok installed adduser adduser 3.129 install ok installed apt apt 2.5.3 install ok installed base-files base-files 12.2 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2-1 install ok installed bsdutils bsdutils 1:2.38.1-1 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.11+git20210903+057cd650a4ed-9 install ok installed debconf debconf 1.5.79 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1 install ok installed debianutils debianutils 5.7-0.3 install ok installed diffutils diffutils 1:3.8-1 install ok installed dpkg dpkg 1.21.9 install ok installed e2fsprogs e2fsprogs 1.46.6~rc1-1 install ok installed findutils findutils 4.9.0-3 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-3 install ok installed gpgv gpgv 2.2.39-1 install ok installed grep grep 3.8-2 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-1 install ok installed liballelecount-perl liballelecount-perl 4.3.0-2 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.5.3 install ok installed libattr1:amd64 libattr1 1:2.5.1-1 install ok installed libaudit-common libaudit-common 1:3.0.7-1.1 install ok installed libaudit1:amd64 libaudit1 1:3.0.7-1.1 install ok installed libb-debug-perl libb-debug-perl 1.26-2 install ok installed libblkid1:amd64 libblkid1 2.38.1-1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.35-1 install ok installed libc6:amd64 libc6 2.35-1 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b1 install ok installed libcap2:amd64 libcap2 1:2.44-1 install ok installed libcom-err2:amd64 libcom-err2 1.46.6~rc1-1 install ok installed libconst-fast-perl libconst-fast-perl 0.014-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.28-2 install ok installed libdata-optlist-perl libdata-optlist-perl 0.112-1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.10 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.264 install ok installed libdevel-cover-perl libdevel-cover-perl 1.38-1 install ok installed libdevel-symdump-perl libdevel-symdump-perl 2.18-4 install ok installed libext2fs2:amd64 libext2fs2 1.46.6~rc1-1 install ok installed libffi8:amd64 libffi8 3.4.3-2 install ok installed libfile-find-rule-perl libfile-find-rule-perl 0.34-2 install ok installed libfile-slurp-perl libfile-slurp-perl 9999.32-1 install ok installed libfile-which-perl libfile-which-perl 1.27-1 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-3 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-2 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.23-2 install ok installed libgdbm6:amd64 libgdbm6 1.23-2 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1 install ok installed libgnutls30:amd64 libgnutls30 3.7.7-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.45-2 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libhtml-parser-perl:amd64 libhtml-parser-perl 3.78-1 install ok installed libhtml-tagset-perl libhtml-tagset-perl 3.20-5 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed libipc-system-simple-perl libipc-system-simple-perl 1.30-1 install ok installed libjson-perl libjson-perl 4.09000-1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.2.5-2.1 install ok installed libmount1:amd64 libmount1 2.38.1-1 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-2 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-2 install ok installed libpam-runtime libpam-runtime 1.5.2-2 install ok installed libpam0g:amd64 libpam0g 1.5.2-2 install ok installed libparams-util-perl libparams-util-perl 1.102-1+b2 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.40-1 install ok installed libpcre3:amd64 libpcre3 2:8.39-14 install ok installed libperl5.34:amd64 libperl5.34 5.34.0-5 install ok installed libpod-coverage-perl libpod-coverage-perl 0.23-2 install ok installed libpod-parser-perl libpod-parser-perl 1.65-1 install ok installed libregexp-ipv6-perl libregexp-ipv6-perl 0.03-3 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b1 install ok installed libselinux1:amd64 libselinux1 3.4-1+b2 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b2 install ok installed libsepol2:amd64 libsepol2 3.4-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-1 install ok installed libss2:amd64 libss2 1.46.6~rc1-1 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-3 install ok installed libsub-exporter-perl libsub-exporter-perl 0.988-1 install ok installed libsub-exporter-progressive-perl libsub-exporter-progressive-perl 0.001013-2 install ok installed libsub-install-perl libsub-install-perl 0.928-2 install ok installed libsystemd0:amd64 libsystemd0 251.4-3 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtest-fatal-perl libtest-fatal-perl 0.016-1 install ok installed libtext-glob-perl libtext-glob-perl 0.11-2 install ok installed libtinfo6:amd64 libtinfo6 6.3+20220423-2 install ok installed libtry-tiny-perl libtry-tiny-perl 0.31-1 install ok installed libudev1:amd64 libudev1 251.4-3 install ok installed libunistring2:amd64 libunistring2 1.0-1 install ok installed liburi-perl liburi-perl 5.12-1 install ok installed libuuid1:amd64 libuuid1 2.38.1-1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.2+dfsg-1 install ok installed login login 1:4.11.1+dfsg1-2 install ok installed logsave logsave 1.46.6~rc1-1 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-1 install ok installed ncurses-base ncurses-base 6.3+20220423-2 install ok installed ncurses-bin ncurses-bin 6.3+20220423-2 install ok installed passwd passwd 1:4.11.1+dfsg1-2 install ok installed perl perl 5.34.0-5 install ok installed perl-base perl-base 5.34.0-5 install ok installed perl-modules-5.34 perl-modules-5.34 5.34.0-5 install ok installed sed sed 4.8-1 install ok installed sysvinit-utils sysvinit-utils 3.05-6 install ok installed tar tar 1.34+dfsg-1 install ok installed tzdata tzdata 2022d-1 install ok installed usr-is-merged usr-is-merged 32 install ok installed usrmerge usrmerge 32 install ok installed util-linux util-linux 2.38.1-1 install ok installed util-linux-extra util-linux-extra 2.38.1-1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-4.1 0m20.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m20.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'apt-get', 'remove', 'libb-debug-perl', 'libconst-fast-perl', 'libdata-optlist-perl', 'libdevel-cover-perl', 'libdevel-symdump-perl', 'libfile-slurp-perl', 'libfile-which-perl', 'libhtml-parser-perl:amd64', 'libhtml-tagset-perl', 'libipc-system-simple-perl', 'libjson-perl', 'libparams-util-perl', 'libpod-coverage-perl', 'libpod-parser-perl', 'libregexp-ipv6-perl', 'libsub-exporter-perl', 'libsub-exporter-progressive-perl', 'libsub-install-perl', 'libtest-fatal-perl', 'libtry-tiny-perl', 'liburi-perl', 'liballelecount-perl'] 0m21.0s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: liballelecount-perl libb-debug-perl libconst-fast-perl libdata-optlist-perl libdevel-cover-perl libdevel-symdump-perl libfile-slurp-perl libfile-which-perl libhtml-parser-perl libhtml-tagset-perl libipc-system-simple-perl libjson-perl libparams-util-perl libpod-coverage-perl libpod-parser-perl libregexp-ipv6-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-install-perl libtest-fatal-perl libtry-tiny-perl liburi-perl 0 upgraded, 0 newly installed, 22 to remove and 0 not upgraded. After this operation, 2509 kB disk space will be freed. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9036 files and directories currently installed.) Removing liballelecount-perl (4.3.0-2) ... Removing libdevel-cover-perl (1.38-1) ... Removing libb-debug-perl (1.26-2) ... Removing libconst-fast-perl (0.014-2) ... Removing libsub-exporter-perl (0.988-1) ... Removing libdata-optlist-perl (0.112-1) ... Removing libpod-coverage-perl (0.23-2) ... Removing libdevel-symdump-perl (2.18-4) ... Removing libfile-slurp-perl (9999.32-1) ... Removing libfile-which-perl (1.27-1) ... Removing libhtml-parser-perl:amd64 (3.78-1) ... Removing libhtml-tagset-perl (3.20-5) ... Removing libipc-system-simple-perl (1.30-1) ... Removing libjson-perl (4.09000-1) ... Removing libparams-util-perl (1.102-1+b2) ... Removing libpod-parser-perl (1.65-1) ... Removing 'diversion of /usr/bin/podselect to /usr/bin/podselect.bundled by libpod-parser-perl' Removing 'diversion of /usr/share/man/man1/podselect.1.gz to /usr/share/man/man1/podselect.bundled.1.gz by libpod-parser-perl' Removing liburi-perl (5.12-1) ... Removing libregexp-ipv6-perl (0.03-3) ... Removing libsub-exporter-progressive-perl (0.001013-2) ... Removing libsub-install-perl (0.928-2) ... Removing libtest-fatal-perl (0.016-1) ... Removing libtry-tiny-perl (0.31-1) ... 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'apt-get', 'remove', 'libb-debug-perl', 'libconst-fast-perl', 'libdata-optlist-perl', 'libdevel-cover-perl', 'libdevel-symdump-perl', 'libfile-slurp-perl', 'libfile-which-perl', 'libhtml-parser-perl:amd64', 'libhtml-tagset-perl', 'libipc-system-simple-perl', 'libjson-perl', 'libparams-util-perl', 'libpod-coverage-perl', 'libpod-parser-perl', 'libregexp-ipv6-perl', 'libsub-exporter-perl', 'libsub-exporter-progressive-perl', 'libsub-install-perl', 'libtest-fatal-perl', 'libtry-tiny-perl', 'liburi-perl', 'liballelecount-perl'] 0m21.0s INFO: Running scripts post_remove 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/post_remove_exceptions'] 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/post_remove_exceptions'] 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'dpkg', '--purge', 'libb-debug-perl', 'libconst-fast-perl', 'libdata-optlist-perl', 'libdevel-cover-perl', 'libdevel-symdump-perl', 'libfile-slurp-perl', 'libfile-which-perl', 'libhtml-parser-perl:amd64', 'libhtml-tagset-perl', 'libipc-system-simple-perl', 'libjson-perl', 'libparams-util-perl', 'libpod-coverage-perl', 'libpod-parser-perl', 'libregexp-ipv6-perl', 'libsub-exporter-perl', 'libsub-exporter-progressive-perl', 'libsub-install-perl', 'libtest-fatal-perl', 'libtry-tiny-perl', 'liburi-perl'] 0m21.0s DUMP: dpkg: warning: ignoring request to remove libb-debug-perl which isn't installed dpkg: warning: ignoring request to remove libconst-fast-perl which isn't installed dpkg: warning: ignoring request to remove libdata-optlist-perl which isn't installed dpkg: warning: ignoring request to remove libdevel-cover-perl which isn't installed dpkg: warning: ignoring request to remove libdevel-symdump-perl which isn't installed dpkg: warning: ignoring request to remove libfile-slurp-perl which isn't installed dpkg: warning: ignoring request to remove libfile-which-perl which isn't installed dpkg: warning: ignoring request to remove libhtml-parser-perl which isn't installed dpkg: warning: ignoring request to remove libhtml-tagset-perl which isn't installed dpkg: warning: ignoring request to remove libipc-system-simple-perl which isn't installed dpkg: warning: ignoring request to remove libjson-perl which isn't installed dpkg: warning: ignoring request to remove libparams-util-perl which isn't installed dpkg: warning: ignoring request to remove libpod-coverage-perl which isn't installed (Reading database ... 8607 files and directories currently installed.) Purging configuration files for libpod-parser-perl (1.65-1) ... dpkg: warning: ignoring request to remove libregexp-ipv6-perl which isn't installed dpkg: warning: ignoring request to remove libsub-exporter-perl which isn't installed dpkg: warning: ignoring request to remove libsub-exporter-progressive-perl which isn't installed dpkg: warning: ignoring request to remove libsub-install-perl which isn't installed dpkg: warning: ignoring request to remove libtest-fatal-perl which isn't installed dpkg: warning: ignoring request to remove libtry-tiny-perl which isn't installed dpkg: warning: ignoring request to remove liburi-perl which isn't installed 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'dpkg', '--purge', 'libb-debug-perl', 'libconst-fast-perl', 'libdata-optlist-perl', 'libdevel-cover-perl', 'libdevel-symdump-perl', 'libfile-slurp-perl', 'libfile-which-perl', 'libhtml-parser-perl:amd64', 'libhtml-tagset-perl', 'libipc-system-simple-perl', 'libjson-perl', 'libparams-util-perl', 'libpod-coverage-perl', 'libpod-parser-perl', 'libregexp-ipv6-perl', 'libsub-exporter-perl', 'libsub-exporter-progressive-perl', 'libsub-install-perl', 'libtest-fatal-perl', 'libtry-tiny-perl', 'liburi-perl'] 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'dpkg', '--purge', 'liballelecount-perl'] 0m21.0s DUMP: dpkg: warning: ignoring request to remove liballelecount-perl which isn't installed 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'dpkg', '--purge', 'liballelecount-perl'] 0m21.0s INFO: Running scripts post_purge 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/post_purge_exceptions'] 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/post_purge_exceptions'] 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'dpkg', '--purge', '--pending'] 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'dpkg', '--purge', '--pending'] 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'dpkg', '--remove', '--pending'] 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'dpkg', '--remove', '--pending'] 0m21.0s INFO: Running scripts post_test 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/post_test_exceptions'] 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'tmp/scripts/post_test_exceptions'] 0m21.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpic6osoyu'] 0m21.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpic6osoyu'] 0m21.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'dpkg-divert', '--list'] 0m21.5s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m21.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'dpkg-divert', '--list'] 0m21.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'apt-get', 'clean'] 0m21.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpic6osoyu', 'apt-get', 'clean'] 0m21.5s DEBUG: Recording chroot state 0m22.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpic6osoyu/dev/shm'] 0m22.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpic6osoyu/dev/shm'] 0m22.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpic6osoyu/dev/console'] 0m22.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpic6osoyu/dev/console'] 0m22.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpic6osoyu/dev/ptmx'] 0m22.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpic6osoyu/dev/ptmx'] 0m22.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpic6osoyu/dev/pts'] 0m22.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpic6osoyu/dev/pts'] 0m22.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpic6osoyu/proc'] 0m22.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpic6osoyu/proc'] 0m22.5s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpic6osoyu'] 0m22.6s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpic6osoyu'] 0m22.6s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpic6osoyu 0m22.6s INFO: PASS: Upgrading between Debian distributions. 0m22.6s INFO: PASS: All tests. 0m22.6s INFO: piuparts run ends. ret=0 End: 2022-09-30 15:18:38 GMT